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High Resolution Single Molecule Measurements Of Transcription And Rna Folding
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Book Synopsis High-resolution, Single-molecule Measurements of Transcription and RNA Folding by : William James Greenleaf
Download or read book High-resolution, Single-molecule Measurements of Transcription and RNA Folding written by William James Greenleaf and published by . This book was released on 2007 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Biophysics of RNA Folding by : Rick Russell
Download or read book Biophysics of RNA Folding written by Rick Russell and published by Springer Science & Business Media. This book was released on 2012-12-09 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume, written by experts in the field, discusses the current understanding of the biophysical principles that govern RNA folding, with featured RNAs including the ribosomal RNAs, viral RNAs, and self-splicing introns. In addition to the fundamental features of RNA folding, the central experimental and computational approaches in the field are presented with an emphasis on their individual strengths and limitations, and how they can be combined to be more powerful than any method alone; these approaches include NMR, single molecule fluorescence, site-directed spin labeling, structure mapping, comparative sequence analysis, graph theory, course-grained 3D modeling, and more. This volume will be of interest to professional researchers and advanced students entering the field of RNA folding.
Book Synopsis Single Molecule RNA Folding Studied with Optical Trapping by : Jeffrey Robert Vieregg
Download or read book Single Molecule RNA Folding Studied with Optical Trapping written by Jeffrey Robert Vieregg and published by . This book was released on 2007 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Visualising RNA Folding Dynamics in Crowded Environments and with Single-molecule Resolution by : Bishnu Paudel
Download or read book Visualising RNA Folding Dynamics in Crowded Environments and with Single-molecule Resolution written by Bishnu Paudel and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Single-molecule Measurements of Transcript Elongation and Termination by RNA Polymerase by : Matthew Herbert Larson
Download or read book Single-molecule Measurements of Transcript Elongation and Termination by RNA Polymerase written by Matthew Herbert Larson and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription by RNAP is highly regulated in both prokaryotic and eukaryotic cells, and the ability of the cell to differentiate and respond to its environment is largely due to this regulation. During elongation, for example, RNAP is known to momentarily halt in response to certain cellular signals, and this pause state has been implicated in the regulation of gene expression in both prokaryotic and eukaryotic organisms. In addition, once RNAP reaches the end of a gene, it must reliably terminate and release the newly-transcribed RNA, providing another potential point of regulation within different cell types. Both of these steps are crucial to ensure proper gene expression. In this dissertation, I focus on transcription elongation by both prokaryotic and eukaryotic RNA polymerases, as well as their regulation through pausing and termination. To probe the role of RNA hairpins in transcriptional pausing, a novel single-molecule "RNA-pulling" assay was used to block the formation of secondary structure in the nascent transcript. Force along the RNA did not significantly affect transcription elongation rates, pause frequencies, or pause lifetimes, indicating that short "ubiquitous" pauses are not a consequence of RNA hairpins. Force-based single-molecule techniques were also used to study the mechanism and energetics of transcription termination in bacteria. The data suggest two separate mechanisms for termination: one that involves hypertranslocation of RNAP along the DNA, and one that involves shearing of the RNA:DNA hybrid within the enzyme. In addition, a quantitative energetic model is presented that successfully predicts the termination efficiency of both wild-type and mutant terminators. Finally, the implementation of a novel optical-trapping assay capable of directly observing transcription by eukaryotic RNA polymerase II (RNAPII) molecules is described. This approach was used to probe the RNAPII nucleotide-addition cycle, as well as the role of the trigger loop (a conserved subdomain) in elongation. The results are consistent with a Brownian ratchet model of elongation which incorporates a secondary NTP binding site, and the trigger loop was found to modulate translocation, NTP binding, and catalysis, as well as substrate selection and mismatch recognition by RNAPII.
Book Synopsis Single-molecule Fluorescence Studies of RNA Folding and Protein-nucleic Acid Assembly by : Gregory Edward Bokinsky
Download or read book Single-molecule Fluorescence Studies of RNA Folding and Protein-nucleic Acid Assembly written by Gregory Edward Bokinsky and published by . This book was released on 2007 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt: Our studies of RNA folding examined the minimal hairpin ribozyme, a system that exhibits a simple two-state behavior. By monitoring the folding and unfolding rates of several mutants and with metal ion titrations, we have developed a coarse-grained picture of an elementary RNA folding transition state. We found that the transition state structure is very compact and stabilized by electrostatic interactions, though native tertiary contacts are either lacking entirely or only partially formed.
Book Synopsis Single Molecule Investigations of Transcriptional Products and Processes by : Hua Yu
Download or read book Single Molecule Investigations of Transcriptional Products and Processes written by Hua Yu and published by . This book was released on 2007 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein and RNA Folding: from Bulk Towards High Throughput Single Molecule Experiments by : Krishnarjun Sarkar
Download or read book Protein and RNA Folding: from Bulk Towards High Throughput Single Molecule Experiments written by Krishnarjun Sarkar and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Single-molecule Studies of RNA Conformations and Cotranscriptional Folding in Adenine Riboswitches by : Kirsten Linnea Frieda
Download or read book Single-molecule Studies of RNA Conformations and Cotranscriptional Folding in Adenine Riboswitches written by Kirsten Linnea Frieda and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA--a ubiquitous and versatile type of biopolymer that is critically involved in many of life's molecular processes--is produced sequentially in single-stranded form during transcription by RNA polymerase and has the propensity to fold back on itself into interesting structures of functional import. In nature, riboswitches are elegant examples of structured RNA that adopt alternate conformations in response to ligand binding and thereby affect gene expression. We have been able to probe riboswitch conformations in novel detail using single-molecule optical-trapping techniques. These experimental approaches supply a unique perspective on folding since the ability to apply force provides an effective handle on the real-time state of individual RNA molecules and a means of modulating that state. In this dissertation, I focus on three studies that explore adenine riboswitch conformations and mechanisms. Specifically, in the first, we dissect the folding landscape of the aptamer (ligand-binding domain) of an adenine riboswitch. Extending this endeavor to full riboswitch sequences, we probe the interplay of a riboswitch aptamer with its downstream expression platform (which executes the switch's regulatory role), and develop methods to do so both during and after transcription. The second study takes full advantage of the latter ability: In a complete adenine riboswitch controlling transcription, we directly observe cotranscriptional folding of the nascent RNA in which the adopted conformation dictates whether or not to terminate transcription. Finally, in a different adenine riboswitch controlling translation, we investigate switch conformational changes and identify a series of competing structural elements that kinetically trap the riboswitch conformation, implying that the initial, cotranscriptional fold of the riboswitch may determine its gene regulatory state. These efforts enhance our understanding of folding architectures in riboswitches, specifically, and in RNA, more broadly. They further highlight the importance of cotranscriptional folding, providing a novel window into the nascent development of RNA conformations.
Book Synopsis Insights Into Large RNA Folding Through Single Molecule Studies of Bacterial RNase P RNA by : Zheng Xie
Download or read book Insights Into Large RNA Folding Through Single Molecule Studies of Bacterial RNase P RNA written by Zheng Xie and published by . This book was released on 2004 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Exploring RNA Folding Dynamics with Carbon Nanotube-based Single-molecule Field-effect Transistors by : Sarah Dubnik
Download or read book Exploring RNA Folding Dynamics with Carbon Nanotube-based Single-molecule Field-effect Transistors written by Sarah Dubnik and published by . This book was released on 2022 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: These methods and protocols were then applied to the studies detailed in Chapter 3, which examines the implications of the thermodynamic and kinetic analyses of RNA stem-loop folding and unfolding as investigated with smFET. Chapter 4 concludes with a brief overview of what has been accomplished and potential future directions for this platform. The work expressed here thus presents a cohesive view of RNA stem-loop folding, integrating the past results of both experimental and computational studies. With this improved smFET methodology, this technique can be applied to many other essential and increasingly complex biological systems to achieve a fuller and richer understanding of the processes that govern life.
Book Synopsis Determining the Rate of Transcription of T7 RNA Polymerase Using Single Molecule Fluorescence Imaging by : Dawn Renee Nicholas
Download or read book Determining the Rate of Transcription of T7 RNA Polymerase Using Single Molecule Fluorescence Imaging written by Dawn Renee Nicholas and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Single-molecule Studies on Transcriptional Elongation in Prokaryotes and Eukaryotes by : Jing Zhou
Download or read book Single-molecule Studies on Transcriptional Elongation in Prokaryotes and Eukaryotes written by Jing Zhou and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription, the process of copying genetic information stored in DNA into RNA, is fundamental to life. It is carried out by an extraordinary nano-machine called RNA polymerase (RNAP). Transcriptional elongation, during which RNAP moves along the DNA, adding one nucleotide at a time to the RNA transcript, is highly dynamic and regulated. The motion of RNAP is discontinuous and interrupted by pauses that play an essential role in gene regulation. Fundamental questions regarding the mechanisms of elongation and its modulation by transcription factors, however, remain unclear. In this dissertation, I focus on using high-resolution, optical trapping techniques to study the mechanisms of transcriptional elongation by both prokaryotic and eukaryotic RNA polymerases at the single-molecule level. First, I describe the studies on how the motion of single E.coli RNAP molecules is modulated by two universally conserved, essential transcription factors (NusA and NusG). From individual transcriptional elongation records, the rates of entering pause states, the pause state lifetimes, and the pause-free elongation speeds can all be extracted. By studying the effects of NusA (and NusG) on these kinetic rates as a function of the applied load, we were able to develop a quantitative kinetic scheme for elongation and pausing. This model not only explains the functions of NusA/NusG, but also provides insight into the mechanism of transcriptional pausing, which had previously been controversial. Second, a novel optical-trapping assay capable of directly probing elongation by individual eukaryotic RNA polymerase II (RNAPII) molecules will be described. We find that the RNAPII trigger loop, an evolutionarily conserved protein subdomain, not only affects each of the three main phases of elongation, namely: substrate binding, translocation, and catalysis; but also plays a critical role in controlling the fidelity of transcription. Our data also support a Brownian ratchet model for elongation which incorporates a secondary nucleotide binding site.
Book Synopsis RNA Folding by : Lucas Gregorio Nivón
Download or read book RNA Folding written by Lucas Gregorio Nivón and published by . This book was released on 2008 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA plays an indispensable enzymatic and structural role in many critical cellular processes, but understanding of its folding mechanism is relatively incomplete. Here I present studies that combine computer predictions based on a simple model of folding with direct observations of single molecules to bring greater understanding to the dynamics and folding pathways of three different RNAs. Many cellular RNAs require a protein co-factor in order to function, so we first use single molecule experimental techniques to understand RNA folding in the presence of a protein co-factor, in chapter I. In parallel, a Go-based technique was developed for the simulation of RNA folding, allowing some of the first computer simulations of the process. The results of these in silico studies are reported in chapter II, for a very small (and computationally accessible) example RNA, the GCAA tetraloop, demonstrating a "zipper" pathway with a putative intermediate. This methodology is then applied to the hairpin ribozyme in chapter III, to derive a model of the folding transition state for the ribozyme and make predictions about the ribozyme dynamics. In chapter III preliminary observations are also made of the high-speed dynamics of the ribozyme in single molecule experiments using two different types of microscopy.
Book Synopsis High Resolution Optical Tweezers for Single Molecule Studies of Hierarchical Folding in the PbuE Riboswitch Aptamer by : Daniel Foster
Download or read book High Resolution Optical Tweezers for Single Molecule Studies of Hierarchical Folding in the PbuE Riboswitch Aptamer written by Daniel Foster and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Hierarchical Dynamics of Individual RNA Helix Base Pair Formation and Disruption by : Jason J. Hon
Download or read book Hierarchical Dynamics of Individual RNA Helix Base Pair Formation and Disruption written by Jason J. Hon and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis explores the RNA folding problem using single-molecule field effect transistors (smFETs) to measure the lifetimes of individual RNA base-pairing rearrangements. In the course of this research, considerable computational, chemical, and engineering contributions were developed so that the single-molecule measurements could be conducted and quantified. These advancements have allowed, on the basis of the smFET data collected herein, the quantification of a kinetic model for RNA stem-loop structures which has been generalized to quantitatively explore the phenomenological observation that an RNA found in the bacillus subtilis strain acts as a metabolite-sensing switch, allowing RNA polymerase to transcribe the messenger RNA when the metabolite is present and preventing transcription when the metabolite is absent. Together, the data presented quantify a simple model for the base pairing rearrangements that underlie RNA folding.
Book Synopsis High Throughput Single Molecule Investigation of Transcription by : Soohong Kim
Download or read book High Throughput Single Molecule Investigation of Transcription written by Soohong Kim and published by . This book was released on 2012 with total page 112 pages. Available in PDF, EPUB and Kindle. Book excerpt:
